def test_find_deadends(read_only_model, store):
"""Expect no deadends to be present."""
store["deadend_metabolites"] = [
met.id for met in consistency.find_deadends(read_only_model)
]
assert len(store["deadend_metabolites"]) == 0,\
"The following metabolites are not consumed by any " \
"reaction of the model: {}".format(
", ".join(store["deadend_metabolites"]))
def test_find_deadends(read_only_model):
"""
Expect no dead-ends to be present.
Dead-ends are metabolites that can only be produced but not consumed by
reactions in the model. They may indicate the presence of network gaps.
"""
ann = test_find_deadends.annotation
ann["data"] = get_ids(consistency.find_deadends(read_only_model))
ann["metric"] = len(ann["data"]) / len(read_only_model.metabolites)
ann["message"] = wrapper.fill(
"""A total of {} ({:.2%}) metabolites are not consumed by any reaction
of the model: {}""".format(
len(ann["data"]), ann["metric"], truncate(ann["data"])))
assert ann["data"] == 0, ann["message"]
def test_find_deadends(model):
"""
Expect no dead-ends to be present.
Dead-ends are metabolites that can only be produced but not consumed by
reactions in the model. They may indicate the presence of network and
knowledge gaps.
Implementation:
Find dead-end metabolites structurally by considering only reaction
equations and reversibility. FBA is not carried out.
"""
ann = test_find_deadends.annotation
ann["data"] = get_ids(consistency.find_deadends(model))
ann["metric"] = len(ann["data"]) / len(model.metabolites)
ann["message"] = wrapper.fill(
"""A total of {} ({:.2%}) metabolites are not consumed by any reaction
of the model: {}""".format(
len(ann["data"]), ann["metric"], truncate(ann["data"])))
assert ann["data"] == 0, ann["message"]
def test_find_deadends(model):
"""
Expect no dead-ends to be present.
Dead-ends are metabolites that can only be produced but not consumed by
reactions in the model. They may indicate the presence of network and
knowledge gaps.
Implementation:
Find dead-end metabolites structurally by considering only reaction
equations and reversibility. FBA is not carried out.
"""
ann = test_find_deadends.annotation
ann["data"] = get_ids(consistency.find_deadends(model))
ann["metric"] = len(ann["data"]) / len(model.metabolites)
ann["message"] = wrapper.fill(
"""A total of {} ({:.2%}) metabolites are not consumed by any reaction
of the model: {}""".format(len(ann["data"]), ann["metric"],
truncate(ann["data"])))
assert ann["data"] == 0, ann["message"]
def test_find_deadends(model, num):
"""Expect the appropriate amount of deadends to be found."""
deadends = consistency.find_deadends(model)
assert len(deadends) == num
def test_find_deadends(model, num):
"""Expect the appropriate amount of deadends to be found."""
deadends = consistency.find_deadends(model)
assert len(deadends) == num